Table 1.

Overview of multiple methods representative for the different SV methodologies currently used. Input types indicate the required data at start being either: De novo assembly (a), Oxford Nanopore (o), PacBio (p), 10X Genomics (x), Hi-C (h), Strand-Seq (t), Optical mapping (c) or Short reads (s)

Category	Name	Input types (a, c, h, o, p, s, tx)	Description	Link	Paper
De novo assembly	Cortex	s	Insertions, deletions, combinations of SNVs—inversions and deletions—rearrangements	http://cortexassembler.sourceforge.net/	[31]
	SGVar	s	Large insertions and deletions, complex SV		[32]
	HySA	p, s	Small (11 to 50 bp) to large (> 50 bp) insertions and deletions, complex SV	https://bitbucket.org/xianfan/hybridassemblysv/overview	[33]
	Assemblytics	a	Insertions and deletions (1 bp to 10 kb), repeat expansions/contractions	https://github.com/MariaNattestad/Assemblytics	[34]
	Paftools	a	Insertions, deletions	https://github.com/lh3/minimap2/tree/master/misc	[35]
	Smartie-sv	a	Insertions, deletions, inversions	https://github.com/zeeev/smartie-sv	[12]
	BreaKmer	s	Insertions, deletions, translocations, inversions, duplications	https://github.com/ccgd-profile/BreaKmer	[36]
	novoBreak	s	Deletions, duplications, inversions, translocations	https://sourceforge.net/projects/novobreak/	[37]
Short-read mapping	BreakDancer	s	Deletions, insertions, inversions, intra-chromosomal and inter-chromosomal translocations	https://github.com/genome/breakdancer	[38]
	BreakSeq		Insertions, deletions, translocations, inversions, duplications	http://sv.gersteinlab.org/breakseq/	[39]
	CREST	s	Insertions, deletions, translocations, inversions, duplications	https://www.stjuderesearch.org/site/lab/zhang	[40]
	DELLY	s	Deletions, inversions, duplications, inter-chromosomal translocations	https://github.com/dellytools/delly	[41]
	EricScript	s	Gene fusion	https://sourceforge.net/projects/ericscript/	[42]
	FusionCatcher	s	Gene fusion	https://github.com/ndaniel/fusioncatcher	[43]
	GRIDSS	s	Insertions, deletions, translocations, inversions, duplications	https://github.com/PapenfussLab/gridss	[44]
	Gustaf	s	Deletions, inversions, duplications, translocation	http://www.seqan.de/apps/gustaf/	[45]
	IDP-fusion	p, s	Gene fusion	https://www.healthcare.uiowa.edu/labs/au/IDP-fusion/	[46]
	JAFFA	p, s	Gene fusion	https://github.com/Oshlack/JAFFA/wiki	[47]
	LUMPY	s	Deletions, duplications, inversions, translocations	https://github.com/arq5x/lumpy-sv	[48]
	Manta	s	Insertions, deletions, translocations, inversions, duplications	https://github.com/Illumina/manta	[49]
	Meerkat	s	Insertions, deletions, translocations, inversions, duplications	http://compbio.med.harvard.edu/Meerkat/	[50]
	Pindel	s	Insertions, deletions, translocations, inversions, duplications	https://github.com/genome/pindel	[51]
	STAR-Fusion	s	Gene fusion	https://github.com/STAR-Fusion/STAR-Fusion/wiki	[52]
	SQUID	s	Gene fusion	https://github.com/Kingsford-Group/squid	[53]
	TARDIS	s	Discovery of tandem and interspersed segmental duplications	https://github.com/BilkentCompGen/tardis	[54]
	TIGRA	s	Insertions, deletions	https://bitbucket.org/xianfan/tigra	[55]
	Tophat-Fusion	s	Gene fusion	http://ccb.jhu.edu/software/tophat/fusion_index.shtml	[56]
	Ulysses	s	Insertions, deletions, translocations, inversions, duplications	https://github.com/gillet/ulysses	[57]
	SvABA	s	Insertion, deletions, somatic rearrangments	https://github.com/walaj/svaba	[58]
Long-read mapping	NanoSV	o	Local SV (LSV): duplications, deletions, inversions; insertions (transposons, intra-chromosomal (> 1 Mb away) and inter-chromosomal insertions)	https://github.com/mroosmalen/nanosv	[59]
	PBHoney	p	Insertions, deletions, duplications, inversions, translocations	https://sourceforge.net/projects/pb-jelly/	[60]
	PBSV	p	Insertions (20 bp to 5 kb), deletions (20 bp to 100 kb), inversions (200 bp to 5 kb), intra-chromosomal (> 100 kb away) and inter-chromosomal translocations, complex SV	https://github.com/PacificBiosciences/pbsv
	SMRT-SV	p	Insertions, deletions, duplications, inversions, translocations	https://github.com/EichlerLab/pacbio_variant_caller	[61]
	Sniffles	o, p	Insertions, deletions, translocations, inversions, duplications, complex SV (nested SV)	https://github.com/fritzsedlazeck/Sniffles	[62]
Multimethods SV caller	FusorSV	s	Combining LUMPY, DELLY, and GenomeSTRiP	https://github.com/TheJacksonLaboratory/SVE	[63]
	MetaSV	s	Combining BreakSeq, Breakdancer, Pindel, CNVnator	http://bioinform.github.io/metasv/	[64]
	Parliament2	s	Combining LUMPY, DELLY, Manta, BreakSeq, CNVnator	https://github.com/dnanexus/parliament2	[65]
	SURVIVOR	a, o, p, s	Can combine/compare any SVs VCF	https://github.com/fritzsedlazeck/SURVIVOR	[10]
Hi-C technology	Hic_breakfinder	h	Detects SVs based on optical mapping, Hi-C, short reads	https://github.com/dixonlab/hic_breakfinder	[66]
	HiCnv	h	Pipeline to identify CNVs from Hi-C data	https://github.com/ay-lab/HiCnv	[67]
	HiCtrans	h	Identify potential translocations using change-point statistics	https://github.com/ay-lab/HiCtrans	[67]
Optical mapping		c	Commercial tools; visualization and analysis of Bionano data	https://bionanogenomics.com/support-page/bionano-access-software/
Strand-Seq technology	Strandseq-InvertR	t	R package to locate putative inversions	https://sourceforge.net/projects/strandseq-invertr/	[68]
10x Genomics	Gemtools	x	Downstream and in-depth analysis of SVs from linked-read data	https://github.com/sgreer77/gemtools	[69]
	GROC-SVs	x	Identify large-scale SVs based on barcode information	https://github.com/grocsvs/grocsvs	[70]
	LongRanger	x	Align reads, call and phase SNPs, indels, identify SVs	https://support.10xgenomics.com/genome-exome/software/downloads/latest	[16]
	NAIBR	x	Identifies novel adjacencies created by SVs events	https://github.com/raphael-group/NAIBR	[71]